Magnesium in the structure of 5-Sme-Du Containing Dna Octamer (pdb 3iki)

The binding sites of Magnesium atom in the structure of 5-Sme-Du Containing Dna Octamer (pdb code 3iki). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3iki structure was solved by J.SHENG, A.E.A.HASSAN, W.ZHANG, J.GAN, Z.HUANG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.3-1.4 Space group P43212 a (A) 42.882 b (A) 42.882 c (A) 23.687 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.8 Rfree (%) 19.4 Magnesium Binding Sites: Magnesium binding site 1 out of 1 in 3iki Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3iki. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Ums2, A: Dg3, A: Hoh26, A: Hoh32, A: Hoh36, A: Hoh45, conact list: Atom Atom Distance (A) Mg C3' A:Ums2 3.50 Mg C6 A:Ums2 4.14 Mg N1 A:Ums2 4.56 Mg C5 A:Ums2 4.49 Mg C1' A:Ums2 4.88 Mg P A:Ums2 4.95 Mg O3' A:Ums2 3.88 Mg OP2 A:Ums2 4.60 Mg C5' A:Ums2 4.76 Mg C2' A:Ums2 4.25 Mg C4' A:Ums2 4.64 Mg O5' A:Ums2 4.06 Mg N9 A:Dg3 4.62 Mg OP1 A:Dg3 4.69 Mg C8 A:Dg3 3.43 Mg P A:Dg3 3.40 Mg N7 A:Dg3 3.87 Mg O4' A:Dg3 4.38 Mg OP2 A:Dg3 2.12 Mg C5' A:Dg3 3.54 Mg C4' A:Dg3 4.57 Mg O5' A:Dg3 3.88 Mg O A:Hoh26 4.59 Mg O A:Hoh32 3.73 Mg O A:Hoh36 2.61 Mg O A:Hoh45 2.68 interactive model: